Thanks for the quick reply.
You were right about the database path.
I have the pep.xml files and the database file in the same folder but
the <database_refresh_timestamp> in the pepXML files was set to absolute
path to the FASTA file. I used sed to fix the database path and it works
now.
Thanks,
Damian
David Shteynberg wrote:
This error means it couldn't read some file. Could be the database
path? Check to make sure all the files are in place. Any older
version you have laying around to try might be next best call.
David
On Apr 7, 2014 7:40 AM, "GATTACA" <[email protected]
<mailto:[email protected]>> wrote:
Hello Everyone,
I'm trying to generate a single ProteinProphet protXML file from
two pepXML files.
The pepXML files are replicates runs of an experiment searched
with the same parameters and database using MASCOT.
When I run this command at the terminal:
ProteinProphet interact-ISO25.pep.xml interact-ISO26.pep.xml
interact-merged.prot.xml
I get the following output and error (in red):
ProteinProphet (C++) by Insilicos LLC and LabKey Software, after
the original Perl by A. Keller (TPP v0.0 Development (DEV) rev 0,
Build 201404071016 (linux))
(xml input) (no FPKM) (report Protein Length) (using degen pep info)
. . . reading in
/home/dfermin/projects/hwchoi/interact-ISO25.pep.xml. . .
. . . read in 0 1+, 51475 2+, 21321 3+, 850 4+, 0 5+, 0 6+, 0 7+
spectra with min prob 0.05
. . . reading in
/home/dfermin/projects/hwchoi/interact-ISO26.pep.xml. . .
. . . read in 0 1+, 33367 2+, 9900 3+, 172 4+, 0 5+, 0 6+, 0 7+
spectra with min prob 0.05
terminate called after throwing an instance of
'boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<std::ios_base::failure>
>'
what(): failed opening file: No such file or directory
This is a new one on me.
The error occurs with the stable release of TPP 4.7.0 and with the
development release (SVN revision 6468).
I'm running TPP on CentOS 6.5 64bit (fully patched).
Any suggestions for a work around?
Thanks in advance,
Damian
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